Heeyoun, I was able to run the sqt2xml program on your sqt file fine. The sqt file you sent me is a little worrisome (see below) but the conversion to pepXML did work. Can you tell me what didn't work for you e.g. did it not generate an sqt file? What error message are you getting? Or did the conversion work for you too but the resulting pepXML file just seemed bad?
If you're not aware, your sqt file has practically no identifications in it; there were around 35 peptide matches out of 12,489 spectral queries. And all of the peptide matches had sequences that just contained A, C, T or G so it appears that you searched a nucleotide database directly without telling ProLuCID to do a codon to amino acid translation. When you translate this file to pepXML, the bulk of the pepXML file has no identifications because that's what's reflected in the input sqt file. Anyways, let me know if you need me to follow-up with this any further. - Jimmy On Mon, Mar 9, 2015 at 8:55 PM, Heeyoun Hwang <tilldaw...@gmail.com> wrote: > Ok, I sent the files to you. > > thx. > > Heeyoun > > 2015년 3월 10일 화요일 오전 2시 22분 11초 UTC+9, Jimmy Eng 님의 말: >> >> Can you make the SQT and sequest.params file available to me? Either >> email it to me directly or make it available for download. I'll take a >> quick look to see what's happening. The mzXML/mzML file is optional; it >> will write instrument info into the resulting pep.xml if present. >> >> - Jimmy >> >> On Sun, Mar 1, 2015 at 9:59 AM, Heeyoun Hwang <tilld...@gmail.com> wrote: >> >>> >>> Hi, >>> >>> Because of my project, I have to search with sequest or ProLuCID in IP2, >>> and generate pep.XML file from *.sqt file for run the peptide prophet. >>> >>> I know that there is no convert program .sqt to .pep.xml in GUI version >>> of TPP. >>> >>> So, I used sqt2xml program in command line, but it is not working. >>> >>> the snapshots of .sqt, .sequest.param, and ms2 files were attached in >>> here. >>> >>> I also tried change the path of FASTA file in param file, but sqt2xml is >>> still not working. >>> >>> Surely I converted mzXL from .RAW with msconvert. All files are in the >>> same directory including .mxML. I also attach the snapshot of my folder. >>> >>> >>> thanks. >>> >>> Heeyoun Hwang. >>> >>> >>> >>> >>> >>> >>> >>> -- >>> You received this message because you are subscribed to the Google >>> Groups "spctools-discuss" group. >>> To unsubscribe from this group and stop receiving emails from it, send >>> an email to spctools-discu...@googlegroups.com. >>> To post to this group, send email to spctools...@googlegroups.com. >>> Visit this group at http://groups.google.com/group/spctools-discuss. >>> For more options, visit https://groups.google.com/d/optout. >>> >> >> -- > You received this message because you are subscribed to the Google Groups > "spctools-discuss" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to spctools-discuss+unsubscr...@googlegroups.com. > To post to this group, send email to spctools-discuss@googlegroups.com. > Visit this group at http://groups.google.com/group/spctools-discuss. > For more options, visit https://groups.google.com/d/optout. > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To unsubscribe from this group and stop receiving emails from it, send an email to spctools-discuss+unsubscr...@googlegroups.com. To post to this group, send email to spctools-discuss@googlegroups.com. Visit this group at http://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
